%1 services

Name Description ELIXIR Node
A Scalable approach to Personal FAIR Data Management and Analysis

Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource.  This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.

Impact of the Study: 

  • Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource.
  • Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. 
  • Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). 
  • Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.
 ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI
A Scalable approach to Personal FAIR Data Management and Analysis

Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource.  This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.

Impact of the Study: 

  • Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource.
  • Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. 
  • Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). 
  • Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.
 ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI
A Scalable approach to Personal FAIR Data Management and Analysis

Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource.  This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.

Impact of the Study: 

  • Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource.
  • Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. 
  • Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). 
  • Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.
 ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI
Data Validation

The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular:

  • Content validation according to minimum information checklists.
  • Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream.
  • Syntactic format validation for Phenotyping data.
  • Semantic validation according to a publicly available ontology.
 ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
Data Validation

The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular:

  • Content validation according to minimum information checklists.
  • Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream.
  • Syntactic format validation for Phenotyping data.
  • Semantic validation according to a publicly available ontology.
 ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
Data Validation

The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular:

  • Content validation according to minimum information checklists.
  • Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream.
  • Syntactic format validation for Phenotyping data.
  • Semantic validation according to a publicly available ontology.
 ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
Data Validation

The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular:

  • Content validation according to minimum information checklists.
  • Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream.
  • Syntactic format validation for Phenotyping data.
  • Semantic validation according to a publicly available ontology.
 ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR integration from a user perspective

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
ELIXIR proof of concept study on the availability of big datasets on remote compute infrastructure

Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC).  The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures.

Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:

  • Deployment and integration of FTS3 by CESNET for use by ELIXIR and integrated into the ELIXIR AAI for use by RDSDS and other activities.
  • Deploy and test in a wide area testbed the first pre-releases from EMBL-EBI of the Reference Data Set Distribution Service (RDSDS) currently being developed by EMBL-EBI within the EUDAT 2020 project.
  • The expansion and performance of the current data transfer testbed to explore FTS3 and RDSDS by identifying ELIXIR nodes (and others) capable of hosting large reference data sets and the reference data sets that will be transferred to test the system

This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar:

This study is associated with: The use of Cloud & VM for training.

 ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland
ELIXIR proof of concept study on the availability of big datasets on remote compute infrastructure

Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC).  The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures.

Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:

  • Deployment and integration of FTS3 by CESNET for use by ELIXIR and integrated into the ELIXIR AAI for use by RDSDS and other activities.
  • Deploy and test in a wide area testbed the first pre-releases from EMBL-EBI of the Reference Data Set Distribution Service (RDSDS) currently being developed by EMBL-EBI within the EUDAT 2020 project.
  • The expansion and performance of the current data transfer testbed to explore FTS3 and RDSDS by identifying ELIXIR nodes (and others) capable of hosting large reference data sets and the reference data sets that will be transferred to test the system

This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar:

This study is associated with: The use of Cloud & VM for training.

 ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland
ELIXIR proof of concept study on the availability of big datasets on remote compute infrastructure

Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC).  The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures.

Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:

  • Deployment and integration of FTS3 by CESNET for use by ELIXIR and integrated into the ELIXIR AAI for use by RDSDS and other activities.
  • Deploy and test in a wide area testbed the first pre-releases from EMBL-EBI of the Reference Data Set Distribution Service (RDSDS) currently being developed by EMBL-EBI within the EUDAT 2020 project.
  • The expansion and performance of the current data transfer testbed to explore FTS3 and RDSDS by identifying ELIXIR nodes (and others) capable of hosting large reference data sets and the reference data sets that will be transferred to test the system

This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar:

This study is associated with: The use of Cloud & VM for training.

 ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland
ELIXIR proof of concept study on the availability of big datasets on remote compute infrastructure

Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC).  The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures.

Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:

  • Deployment and integration of FTS3 by CESNET for use by ELIXIR and integrated into the ELIXIR AAI for use by RDSDS and other activities.
  • Deploy and test in a wide area testbed the first pre-releases from EMBL-EBI of the Reference Data Set Distribution Service (RDSDS) currently being developed by EMBL-EBI within the EUDAT 2020 project.
  • The expansion and performance of the current data transfer testbed to explore FTS3 and RDSDS by identifying ELIXIR nodes (and others) capable of hosting large reference data sets and the reference data sets that will be transferred to test the system

This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar:

This study is associated with: The use of Cloud & VM for training.

 ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland
ELIXIR proof of concept study on the availability of big datasets on remote compute infrastructure

Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC).  The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures.

Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:

  • Deployment and integration of FTS3 by CESNET for use by ELIXIR and integrated into the ELIXIR AAI for use by RDSDS and other activities.
  • Deploy and test in a wide area testbed the first pre-releases from EMBL-EBI of the Reference Data Set Distribution Service (RDSDS) currently being developed by EMBL-EBI within the EUDAT 2020 project.
  • The expansion and performance of the current data transfer testbed to explore FTS3 and RDSDS by identifying ELIXIR nodes (and others) capable of hosting large reference data sets and the reference data sets that will be transferred to test the system

This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar:

This study is associated with: The use of Cloud & VM for training.

 ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland
Enabling the reuse, extension, scaling, and reproducibility of scientific workflows (2018-cwl)

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

  1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
  2. extend the current CWL workflows to enable greater reuse;
  3. enhance the execution frameworks to improve both deployment and scalability;
  4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

 ELIXIR France, ELIXIR UK, EMBL-EBI, ELIXIR Finland
Enabling the reuse, extension, scaling, and reproducibility of scientific workflows (2018-cwl)

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

  1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
  2. extend the current CWL workflows to enable greater reuse;
  3. enhance the execution frameworks to improve both deployment and scalability;
  4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

 ELIXIR France, ELIXIR UK, EMBL-EBI, ELIXIR Finland
Enabling the reuse, extension, scaling, and reproducibility of scientific workflows (2018-cwl)

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

  1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
  2. extend the current CWL workflows to enable greater reuse;
  3. enhance the execution frameworks to improve both deployment and scalability;
  4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

 ELIXIR France, ELIXIR UK, EMBL-EBI, ELIXIR Finland
Enabling the reuse, extension, scaling, and reproducibility of scientific workflows (2018-cwl)

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

  1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
  2. extend the current CWL workflows to enable greater reuse;
  3. enhance the execution frameworks to improve both deployment and scalability;
  4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

 ELIXIR France, ELIXIR UK, EMBL-EBI, ELIXIR Finland
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expanding the Galaxy: meeting (the needs of) ELIXIR Communities

As data analysis is now common place in life sciences, we need to develop scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

The ELIXIR Communities bring together domain experts. This is an ideal way to identify and develop standard workflows for commonly used analyses in that specific domain. Since summer 2016 the Galaxy Training Network has been collecting and further developing training material for analysis in, development and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals

  1. Expand the portfolio of Community workflows, including training material to describe them
  2. Facilitate access to data in Core Data Resources and Deposition Databases
  3. Improve the user experience of the Galaxy platform

Background

Galaxy is a workflow management system that 1) provides support for reproducible science, 2) facilitates sharing of data and results and 3) removes the need for users to compile and install tools. Galaxy offers a user-interface, through a web browser, in which virtually any command line tool can be integrated. This is done by defining the inputs, outputs and parameters in a wrapper script. As analyses usually consist of multiple steps, tools can be composed in workflows, which facilitates the processing of multiple samples and reproduction of analyses. Galaxy is available as a world-wide free-to-use online portal, following open-source policy development and can be freely downloaded for a local installation.

The Galaxy workflow system is extensively used as part of national infrastructures in several ELIXIR Nodes. Galaxy itself is considered an integral part of bioinformatics infrastructure by many bioinformatics researchers and core facility groups because it enables simplified access to data and analysis tools under a single “intuitive” interface. Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) are working since several years with Goblet and the ELIXIR Training Platform to enhance and deliver first-class training to the Scientific community - targeting not only scientists but also developers and admins. 

Goals

In this project we will engage with ELIXIR Communities that are not yet well represented in the Galaxy ecosystem. The aim is to deliver deployable workflows for commonly used analysis in these scientific domains. This encompasses the whole stack needed: availability of tools in Galaxy and exemplar workflows as well as access to data, both reference data and published research data.

In collaboration with the Training platform and the involved Community, we will do a gap analysis to identify which components of the stack are missing or can be improved. We will bring experts of the scientific discipline, training and Galaxy together in a hackathon to address this and develop training materials to document the developed workflows and enable trainings. This training material will be included in the Galaxy Training Network initiative https://training.galaxyproject.org (which is indexed by TeSS). As through these events we are bringing together established and potential new trainers, we will combine this with a Train the Trainer event.

We will also organise trainings using already existing and newly developed material, targeted towards researchers within this community. We also will make use of these events to assess the usability of Galaxy.

WP1 : Enable commonly used workflows for Communities

The bulk of the funding in this project will be allocated to organize events, bringing together experts of a scientific Community, Galaxy and the Training platform. We have selected five Communities (Plant, Metagenomics, Metabolomics , Proteomics and 3D BioInfo), for each one we will organize three events : a hackathon, a training for researchers and a Train-the-Trainer event. To reduce costs and travelling, we envision that these are organised co-located and back-to-back (per community).

The aim of the hackathon is to address (selected) issues that have been identified through a gap analysis, to enable researchers to perform standard analysis in Galaxy. This is done in preparation of the hackathon, in collaboration with all stakeholders involved. These issues can range from wrapping tools into Galaxy, making workflows, providing visualisation plugins, etc. Also access to data is in scope, in collaboration with WP2 of this proposal. To disseminate the work done, training materials will be developed using these developments.

We will ensure all developments are appropriately referenced in ELIXIR registries, building on the expertise available in ELIXIR, in the Tools and Interoperability Platform: tools will be added to bio.tools and, if applicable, containers will be made available in BioContainers, and workflows will be registered in MyExperiment. This will be done in alignment with and complementary to the development of this infrastructure in EOSC-Life (WP Tools Collaboratory).

We will combine this hackathon with a Train-the-Trainer event, building on the expertise of the Training Platform. This aims to improve the teaching skills of the trainers as well as make them more familiar with the Galaxy platform and how it can support trainers and training events.

WP2 : Access to data

Access to data is currently a major bottleneck for many users. In collaboration with data providers, we will incorporate ELIXIR Deposition Databases and confer with the communities what additional resources are of interest.

Access to data from UCSC has been integrated in Galaxy through dedicated additions to the web pages that allow searching this resource. Based on work started in the PheNoMeNal projects, a Galaxy tool is developed to communicate with MetaboLights. Dedicated tools can provide both the ability to retrieve as submit data to Deposition Databases. However, these current approaches are very labour intensive to scale to all ELIXIR Core Data Resources and Deposition Databases, as well as difficult to maintain.

The Omics Discovery Index (OmicsDI, http://omicsdi.org) provides an integrated metadata resource for 20 different databases with currently 450,000 datasets (October 2018), including four Elixir Core Data Resources (ArrayExpress, EGA, ENA, PRIDE), as well as two additional Elixir Deposition Databases (BioModels, MetaboLights). OmicsDI already provides web service access for search and metadata retrieval across all integrated resources. To facilitate data access in Galaxy workflows, we will add a method to OmicsDI to provide the direct data download URLs for any selected dataset. This method will be integrated into Galaxy workflows to automatically download and process relevant datasets selected based on standardised metadata criteria.  

The proposed integration of OmicsDI in Galaxy as a data source allows to enable access to datasets from different data sources through a common entrypoint. The data access method that will be developed in this project will be independent of Galaxy. This makes integration in other workflow systems or scripts possible, broadening the impact beyond the Galaxy community. We envision this work as a step towards a common way to (programmatically) access ELIXIR Core Data Resources and Deposition Databases, based on both keyword search as well as commonly used identifiers.

This aligns to the objectives of the ELIXIR Interoperability Platform and Galaxy Community. This will result in improved access to ELIXIR Core Data Resources and Deposition Databases for the whole life science community, as well as a specific integration in Galaxy. The work will be disseminated through e.g. usage in the developed training materials (WP1). In consultation with the ELIXIR Hub, a dedicated webinar can be organised.

 ELIXIR Spain, ELIXIR Portugal, ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, EMBL-EBI, ELIXIR UK, ELIXIR Belgium , ELIXIR Greece, ELIXIR Norway, ELIXIR Czech Republic
Expertise building on Galaxy Administration, Pulsar, and CernVM File System

UseGalaxy.eu (https://usegalay.eu) is the main European Galaxy public instance, providing more than 2000 tools belonging to different bioinformatics research fields. Tens of smaller scale Galaxy instances are also available across Europe, while ELIXIR-IT is launching its first own Galaxy on-demand cloud service at the ReCaS Cloud and GARR Cloud facilities. It is therefore critical for ELIXIR Nodes to quickly build expertise in Galaxy servers administration and to continue developing the technological infrastructure needed to sustain the European Galaxy network.

The ELIXIR-IT "Laniakea@GARRCloud" program, currently ongoing, aims to deploy a Laniakea Galaxy on-demand service also at GARR Cloud, following the one already available at ReCaS Cloud, and the concurrent installation of a Pulsar endpoint to allow the execution of UseGalaxy.eu jobs on GARR Cloud, together with the deployment of a mirror (stratum 1) of the Galaxy CVMFS System server. Both UseGalaxy.eu and Pulsar network development and maintenance are driven by the Freiburg Galaxy Team (ELIXIR-DE).

This Staff Exchange's purpose is to allow "Laniakea@GARRCloud" developer and Laniakea lead developer to travel to Freiburg, where the Galaxy Europe Freiburg Team (ELIXIR-DE) is based, for a couple of months in order to quickly build expertise and receive advanced training on Pulsar, CVMFS and their deployment on Cloud infrastructures.

We expect that this Staff Exchange will foster a smoother and faster integration of ELIXIR-IT activities within the ELIXIR Galaxy community, establishing more direct links between the Italian and the German ELIXIR Nodes and allowing the creation of a robust and lasting collaboration between the two Nodes on Galaxy-related topics.

 ELIXIR Italy, ELIXIR Germany
Expertise building on Galaxy Administration, Pulsar, and CernVM File System

UseGalaxy.eu (https://usegalay.eu) is the main European Galaxy public instance, providing more than 2000 tools belonging to different bioinformatics research fields. Tens of smaller scale Galaxy instances are also available across Europe, while ELIXIR-IT is launching its first own Galaxy on-demand cloud service at the ReCaS Cloud and GARR Cloud facilities. It is therefore critical for ELIXIR Nodes to quickly build expertise in Galaxy servers administration and to continue developing the technological infrastructure needed to sustain the European Galaxy network.

The ELIXIR-IT "Laniakea@GARRCloud" program, currently ongoing, aims to deploy a Laniakea Galaxy on-demand service also at GARR Cloud, following the one already available at ReCaS Cloud, and the concurrent installation of a Pulsar endpoint to allow the execution of UseGalaxy.eu jobs on GARR Cloud, together with the deployment of a mirror (stratum 1) of the Galaxy CVMFS System server. Both UseGalaxy.eu and Pulsar network development and maintenance are driven by the Freiburg Galaxy Team (ELIXIR-DE).

This Staff Exchange's purpose is to allow "Laniakea@GARRCloud" developer and Laniakea lead developer to travel to Freiburg, where the Galaxy Europe Freiburg Team (ELIXIR-DE) is based, for a couple of months in order to quickly build expertise and receive advanced training on Pulsar, CVMFS and their deployment on Cloud infrastructures.

We expect that this Staff Exchange will foster a smoother and faster integration of ELIXIR-IT activities within the ELIXIR Galaxy community, establishing more direct links between the Italian and the German ELIXIR Nodes and allowing the creation of a robust and lasting collaboration between the two Nodes on Galaxy-related topics.

 ELIXIR Italy, ELIXIR Germany
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Galaxy Community Implementation Study

This Implementation Study is to establish the Galaxy ELIXIR Community to promote exchanges between the several European initiatives around the framework Galaxy. 

  • Build a comprehensive community among the developers and administrators, and
  • Collaborate with trainers and other ELIXIR Communities and platforms.
  • To hire a dedicated Community Manager to facilitate interactions and dissemination of information.

To develop a network of Galaxy based on: 

  • national Galaxy instances already available or planned in the Nodes
  • best-practices
  • shared data and with a unified authentication

 This tudy will also identify technical developments that will help integration with ELIXIR Services (ISA-TAB and selected Core Data Resources) and improve visualisation infrastructure.

.

 ELIXIR Belgium , ELIXIR France, ELIXIR Germany, ELIXIR Norway, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Slovenia
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

 ELIXIR Belgium , ELIXIR France, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Denmark
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Strengthen Data Management in Galaxy

This proposal focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. We will leverage existing technologies and services in ELIXIR and complement ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data portal, EOSC Life, etc.) while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Among the goals, we aim to make the Galaxy Data Libraries more scalable and further improve the reusability features of the platform by metadata enrichment. The Galaxy metadata system will be extended to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub).

A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human data. Therefore, support for user-level encrypted data processing will also be added to allow for the analysis of sensitive data. To this end, we will include an encryption layer into the Pulsar network and enhance performance by increasing the data locality of distributed Galaxy analyses through a prototype data caching network.

These data management-related features and improvements aim to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses. The Galaxy Community has demonstrated the ability to sustain a fast rollout of novel fit-for-purpose features for the needs of European researchers, a trend we intend to continue with this proposal.

Join this Implementation Study
 ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR UK
Tools integration under Galaxy and tools development for the integration and querying of heterogeneous QTL data

This collaborative project focuses on two issues related to bioinformatics. The first issue concerns the availability of the virAnnot pipeline (doi:10.1094/PBIOMES-07-19-0037-A) that was developed in the Virology team (INRAE UMR 1332) for the CATI BARIC community and the collaborators of the Virology team. This pipeline, intended for everyone, is however only used by bioinformaticians as it can only be used on command line. The first objective of this project is thus the integration of this pipeline in the GALAXY environment which is widely used by the scientific community for the analysis of HTS data in viral metagenomics. The Bioinformatics group of Wageningen University is a major pole of the European programme for the provision of bioinformatics resources in life sciences and is involved in training under Galaxy. It will be possible to follow the trainings given on site and interact with the trainers. At the end of the mission, the pipeline will be implemented in Galaxy and will be included in the analysis offer of the Galaxy platform hosted on the Genouest cluster in Rennes, France, which is part of the French Institute of Bioinformatics (IFB), the French Node of ELIXIR, making viral metagenomics analyses easily accessible to the CATI BARIC community and to all users of the GALAXY environment.

The second issue concerns the accurate identification of QTL regions. Indeed, a QTL region covers a rather large gene region with many genes, so it is difficult to find the real causal gene. This is often done using experimental fine mapping, but this method is laborious. The second objective of this project is therefore to develop a method to prioritize the genes of a QTL region in order to identify more precisely the causal gene affecting the trait. An in silico method will be developed to improve the resolution of a QTL analysis. This method will be based on prior knowledge from literature/databases via semantic web technologies and will take the form of a data query tool. The developments of Dr. Harm Nijveen's workgroup are based on Semantic Web and Linked Open Data (LOD) technologies. The tool developments will be based on two existing platforms, WormQTL2 (doi:10.1093/database/baz149) and AraQTL (doi:10.1111/tpj.13457), populated with data on C. elegans and A. thaliana. These databases can then be used and enriched with data on fruit trees, which are present in the Virology team. This work will enhance interactions between the Virology team and the Bioinformatics group as well as strengthening skills around the semantic web and data interoperability for both partners.

 ELIXIR France, ELIXIR Netherlands
Tools integration under Galaxy and tools development for the integration and querying of heterogeneous QTL data

This collaborative project focuses on two issues related to bioinformatics. The first issue concerns the availability of the virAnnot pipeline (doi:10.1094/PBIOMES-07-19-0037-A) that was developed in the Virology team (INRAE UMR 1332) for the CATI BARIC community and the collaborators of the Virology team. This pipeline, intended for everyone, is however only used by bioinformaticians as it can only be used on command line. The first objective of this project is thus the integration of this pipeline in the GALAXY environment which is widely used by the scientific community for the analysis of HTS data in viral metagenomics. The Bioinformatics group of Wageningen University is a major pole of the European programme for the provision of bioinformatics resources in life sciences and is involved in training under Galaxy. It will be possible to follow the trainings given on site and interact with the trainers. At the end of the mission, the pipeline will be implemented in Galaxy and will be included in the analysis offer of the Galaxy platform hosted on the Genouest cluster in Rennes, France, which is part of the French Institute of Bioinformatics (IFB), the French Node of ELIXIR, making viral metagenomics analyses easily accessible to the CATI BARIC community and to all users of the GALAXY environment.

The second issue concerns the accurate identification of QTL regions. Indeed, a QTL region covers a rather large gene region with many genes, so it is difficult to find the real causal gene. This is often done using experimental fine mapping, but this method is laborious. The second objective of this project is therefore to develop a method to prioritize the genes of a QTL region in order to identify more precisely the causal gene affecting the trait. An in silico method will be developed to improve the resolution of a QTL analysis. This method will be based on prior knowledge from literature/databases via semantic web technologies and will take the form of a data query tool. The developments of Dr. Harm Nijveen's workgroup are based on Semantic Web and Linked Open Data (LOD) technologies. The tool developments will be based on two existing platforms, WormQTL2 (doi:10.1093/database/baz149) and AraQTL (doi:10.1111/tpj.13457), populated with data on C. elegans and A. thaliana. These databases can then be used and enriched with data on fruit trees, which are present in the Virology team. This work will enhance interactions between the Virology team and the Bioinformatics group as well as strengthening skills around the semantic web and data interoperability for both partners.

 ELIXIR France, ELIXIR Netherlands
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany
Using clouds and VMs for bioinformatics training

Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course.

Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting.

Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner.

As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider.

This study is now complete, the final report and other documents will be added as they are available. 

 ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium , ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany